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tih_rna_sample_00375_23LGNLLT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0002/A23LGNLLT4/nfcore_rnafusion_100M__5f1fa79--20260304-095416/QC/picard/tih_rna_sample_00375_23LGNLLT4_1_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0002_5f1fa79
Published
Mar 09, 2026 3:03 PM

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## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT tih_rna_sample_00375_23LGNLLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00375_23LGNLLT4_1_rna_metrics.txt --TMP_DIR ./tmp --MINIMUM_LENGTH 500 --RRNA_FRAGMENT_PERCENTAGE 0.8 --METRIC_ACCUMULATION_LEVEL ALL_READS --END_BIAS_BASES 100 --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
## htsjdk.samtools.metrics.StringHeader
# Started on: Mon Mar 09 20:52:06 GMT 2026

## METRICS CLASS	picard.analysis.RnaSeqMetrics
PF_BASES	PF_ALIGNED_BASES	RIBOSOMAL_BASES	CODING_BASES	UTR_BASES	INTRONIC_BASES	INTERGENIC_BASES	IGNORED_READS	CORRECT_STRAND_READS	INCORRECT_STRAND_READS	NUM_R1_TRANSCRIPT_STRAND_READS	NUM_R2_TRANSCRIPT_STRAND_READS	NUM_UNEXPLAINED_READS	PCT_R1_TRANSCRIPT_STRAND_READS	PCT_R2_TRANSCRIPT_STRAND_READS	PCT_RIBOSOMAL_BASES	PCT_CODING_BASES	PCT_UTR_BASES	PCT_INTRONIC_BASES	PCT_INTERGENIC_BASES	PCT_MRNA_BASES	PCT_USABLE_BASES	PCT_CORRECT_STRAND_READS	MEDIAN_CV_COVERAGE	MEDIAN_5PRIME_BIAS	MEDIAN_3PRIME_BIAS	MEDIAN_5PRIME_TO_3PRIME_BIAS	SAMPLE	LIBRARY	READ_GROUP
24085740683	23747591421	20102	21125790641	1347233282	1153893108	120654288	0	0	0	2522623	79768870	443265	0.030655	0.969345	0.000001	0.889597	0.056731	0.04859	0.005081	0.946329	0.933043	0	0.512681	0.498603	0.780872	0.780328			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.309304
1	0.342947
2	0.394955
3	0.448493
4	0.49115
5	0.531651
6	0.589281
7	0.643388
8	0.700745
9	0.754786
10	0.803211
11	0.842505
12	0.886819
13	0.928024
14	0.961091
15	0.995223
16	1.02559
17	1.045401
18	1.061114
19	1.070202
20	1.085834
21	1.101554
22	1.12052
23	1.13778
24	1.147517
25	1.156815
26	1.161183
27	1.161847
28	1.159208
29	1.15802
30	1.167952
31	1.170184
32	1.177712
33	1.182777
34	1.183365
35	1.181013
36	1.176815
37	1.17178
38	1.172646
39	1.172173
40	1.178024
41	1.179854
42	1.184364
43	1.193771
44	1.196601
45	1.211408
46	1.210963
47	1.210973
48	1.208791
49	1.195654
50	1.180657
51	1.173778
52	1.164142
53	1.155096
54	1.154199
55	1.153207
56	1.149444
57	1.1467
58	1.14203
59	1.13347
60	1.123111
61	1.122374
62	1.125158
63	1.119283
64	1.119813
65	1.120663
66	1.112292
67	1.103369
68	1.094352
69	1.093314
70	1.080614
71	1.068952
72	1.060792
73	1.054272
74	1.044021
75	1.0386
76	1.030058
77	1.020981
78	1.017826
79	1.009252
80	1.002395
81	0.990592
82	0.982549
83	0.972383
84	0.959944
85	0.945396
86	0.929624
87	0.921445
88	0.903557
89	0.885476
90	0.864469
91	0.843897
92	0.816543
93	0.788286
94	0.761168
95	0.728767
96	0.697717
97	0.663593
98	0.631169
99	0.595825
100	0.553159